I believe it would have been nice if they were to do more with X and Y's version of Global Link. In Black and White, we've had a ton of things, such as putting Pokémon into sleep, having them transferred, befriending other Pokémon so that they would eventually join you (if I remember correctly; could be wrong), and so forth; if they had done something similar with these two, I believe it would've gone a long way.
One thing that comes to mind right off the bat is character-customization. Of course, it was great to be accessing this feature in-game and personalize our player any way we choose, but one down side of that is, we were limited to our range of clothes and accessories (due to cartridge memory capacity), but if we were to do all these things online and later have our changes get transferred into games, lots of these restrictions would be lifted, I feel, since putting limit to customization things won't likely be required.
Current version of Global Link definitely isn't bad, however, but there's always room for improvements.